On 09/25/2010 08:22 AM, heyi xiao wrote:
> Thanks Valerie,
> Now I understand the readQualityScore. I ran your example code, the
> first few steps worked well till the report generation step. I got
the
> same error as in my own example.
>
> > report(res)
> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""),
width, :
> unable to start device JPEG
> In addition: Warning message:
> In jpeg(file.path(imgDir, jpegFile), ...) :
> no jpeg support in this version of R
>
> It seems to me that I will have to ungrade to R 2.12. If I ungrade,
> the bioconductor I get will be the devel version using biocLite(),
right?
>
> Below is my current session info. Thanks again for the help!
>
Yes, if you install R 2.12 and biocLite("ShortRead") you will get the
most recent devel version of ShortRead.
However, your problem appears to be with report generation only and
not
creating the qa() object so
using the devel version will not help us here. I previously thought
you
were having problems
generating a qa() object which is why I provided the example code.
Sorry
for the misunderstanding.
The report generation requires jpeg capabilities and you don't appear
to
have this on the
remote machine that you are running on. I think the quickest fix would
be to save
the qa() object as an .rda file then move this file to your local R
machine. (This .rda file
is small even if your data are large.) You can then load() the .rda
into
an R session on
your local machine and generate the report there. It is much more
likely
that you
will have jpeg support on your local machine.
I sent an email yesterday (9/25) where I mention another option of
recompiling R
with jpeg support enabled.
Hopefully the .rda file option works for you. Let me know how it goes.
Valerie
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
> [4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US
> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] CSAMA10_0.0.3 chipseq_0.4.1
GenomicFeatures_1.0.10
> [4] biomaRt_2.4.0 BSgenome_1.16.5
EatonEtAlChIPseq_0.0.1
> [7] rtracklayer_1.8.1 RCurl_1.4-3 bitops_1.0-4.1
> [10] ShortRead_1.6.2 Rsamtools_1.0.8 lattice_0.18-8
> [13] Biostrings_2.16.9 GenomicRanges_1.0.9 IRanges_1.6.17
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 DBI_0.2-5 grid_2.11.1 hwriter_1.2
RSQLite_0.9-2
> [6] tools_2.11.1 XML_3.1-1
>
>
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